adding stroke does add port timing especially in the transfers, the cylinder can be run with a spacer and/or gaskets that does not raise the cylinder as much as a typical stroker spacer which then helps keep the port timing from getting to high. That is what I did on Jon's ProX motor, but the piston does come out of the cylinder some and the head must be recut to account for the piston.
you still have not really explained what you are looking for in the powerband, I take it you are wanting more low-mid range power if you trail ride, the trx9 porting is a dune porting and that means port timing should favor more mid-upper power, MX porting will be slightly less so more than likely the base gasket would need to be thinner and the base of the cylinder would need to be cut to lower the cylinder so port timings can favor a more MX powerband.
I think you should just play with tuning the carb with different needles maybe add a little timing by buying a adjustable counter balancer holder for the pickup and also improve your tailpipe bend that you did along with a larger perforated screen.
with those 3 changes I think you will see a noticeable change in power once everything is optimized
